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- PDB-3r75: Crystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC... -

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Basic information

Entry
Database: PDB / ID: 3r75
TitleCrystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC) synthase PhzE from Burkholderia lata 383 in complex with benzoate, pyruvate, glutamine and contaminating Zn2+
ComponentsAnthranilate/para-aminobenzoate synthases component I
KeywordsLYASE / BIOSYNTHETIC PROTEIN / ammonia channel / chorismate / type 1 glutamine amidotransferase / phenazine biosynthesis / synthase
Function / homology
Function and homology information


anthranilate synthase / anthranilate synthase activity / biosynthetic process / glutamine metabolic process / metal ion binding
Similarity search - Function
Anthranilate synthase/para-aminobenzoate synthase like domain / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. ...Anthranilate synthase/para-aminobenzoate synthase like domain / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / PHOSPHATE ION / PYRUVIC ACID / anthranilate synthase
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLi, Q.A. / Mavrodi, D.V. / Thomashow, L.S. / Roessle, M. / Blankenfeldt, W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Ligand Binding Induces an Ammonia Channel in 2-Amino-2-desoxyisochorismate (ADIC) Synthase PhzE.
Authors: Li, Q.A. / Mavrodi, D.V. / Thomashow, L.S. / Roessle, M. / Blankenfeldt, W.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthranilate/para-aminobenzoate synthases component I
B: Anthranilate/para-aminobenzoate synthases component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,39913
Polymers140,5852
Non-polymers81411
Water14,196788
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-132 kcal/mol
Surface area45220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)259.710, 94.512, 53.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Anthranilate/para-aminobenzoate synthases component I


Mass: 70292.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. (bacteria) / Strain: 383 / Gene: Bcep18194_B1570 / Plasmid: pET19modTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q396C7, anthranilate synthase

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Non-polymers , 6 types, 799 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 788 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1 M HEPES, 0.2 M Mg-chloride, 22% isopropanol, pre-incubation on ice for 30' with 50 mM Mg-chloride, 20 mM glutamine, 20 mM chorismate, streak-seeding, pH 7.1, vapor diffusion, hanging drop, temperature 276K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.625 Å / Num. obs: 77637 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.509 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.20.2353.74415791902798.3
2.2-2.30.1874.75350091590998.6
2.3-2.40.1515.74295931336198.8
2.4-2.50.1266.9252261136899
2.5-2.60.1038.2421558971599
2.6-30.07211.33603502709199
3-40.03919.49643862897098.4
4-60.02926.13332041476297.3
6-80.02527.038076355596.9
8-120.02231.314098181496.1
12-160.02231.3798044495.5
16-180.02232.225810796.4
18-200.02429.52884790.4
20

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0077refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.625 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 8.255 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 3934 5.1 %RANDOM
Rwork0.1468 73703 --
obs0.1495 77637 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 122.08 Å2 / Biso mean: 40.0817 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.26 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 0 45 788 10293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0219933
X-RAY DIFFRACTIONr_bond_other_d0.0070.026705
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.96113547
X-RAY DIFFRACTIONr_angle_other_deg2.4413.00116225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52551314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16322.56461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.802151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.92215106
X-RAY DIFFRACTIONr_chiral_restr0.1180.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111377
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022115
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 282 -
Rwork0.175 5374 -
all-5656 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.96140.35730.33781.06320.25320.61870.0317-0.0578-0.08390.0927-0.0173-0.09270.00790.0432-0.01440.0814-0.0064-0.01660.07540.01290.013721.900332.660934.0113
21.2135-0.0135-0.29240.71650.15420.85480.04740.08650.18150.04230.02760.0121-0.0355-0.0612-0.0750.038-0.004-0.010.01720.02950.056860.268254.732610.9428
34.45540.8694-0.05632.2202-0.14711.7047-0.0764-0.3846-0.42480.16790.0603-0.17510.1517-0.11260.01610.12330.0259-0.02370.06840.03890.061573.693334.958915.717
43.34210.6932-0.20341.195-0.12161.2131-0.22120.28980.2462-0.20340.20150.1581-0.10320.04060.01960.1927-0.0552-0.04920.12880.02960.032712.386236.04911.5989
51.79670.023-0.57510.836-0.08871.23430.01680.08590.0598-0.0631-0.0329-0.2336-0.00560.03040.01610.01140.00850.02210.01310.01820.111391.560645.284-5.7563
61.43620.55620.27011.48020.08380.51950.0012-0.036-0.0171-0.0484-0.00990.22850.0189-0.06740.00860.0498-0.027-0.03090.02260.00890.0618-8.754316.650622.425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 397
2X-RAY DIFFRACTION1A700 - 702
3X-RAY DIFFRACTION1A900
4X-RAY DIFFRACTION2B7 - 397
5X-RAY DIFFRACTION2B700 - 702
6X-RAY DIFFRACTION2B900
7X-RAY DIFFRACTION3A398 - 431
8X-RAY DIFFRACTION4B398 - 431
9X-RAY DIFFRACTION5A442 - 636
10X-RAY DIFFRACTION6B440 - 636

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